rs4803224

Variant names:

• chr19-39262374-G-C
• rs4803224

Your query was ambiguous. Multiple possible variants found:

• chr19-39262374-G-C
• chr19-39262374-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 151,726 control chromosomes in the GnomAD database, including 3,508 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3508 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30038 AN: 151608 Hom.: 3513 Cov.: 30

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.237

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.198 AC: 30038 AN: 151726 Hom.: 3508 Cov.: 30 AF XY: 0.197 AC XY: 14576 AN XY: 74114

African (AFR) AF: 0.0879 AC: 3642 AN: 41410

American (AMR) AF: 0.303 AC: 4607 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3472

East Asian (EAS) AF: 0.107 AC: 552 AN: 5162

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4812

European-Finnish (FIN) AF: 0.181 AC: 1901 AN: 10484

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16407 AN: 67886

Other (OTH) AF: 0.235 AC: 493 AN: 2102

Alfa AF: 0.218 Hom.: 495

Bravo AF: 0.204

Asia WGS AF: 0.164 AC: 571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4803224; hg19: chr19-39753014;